3FX8

Distinct recognition of three-way DNA junctions by a thioester variant of a metallo-supramolecular cylinder ('helicate')

PDB DOI: https://doi.org/10.2210/pdb3FX8/pdb
NAKB: 3FX8

Classification: DNA
Mutation(s): No

Deposited: 2009-01-20 Released: 2010-03-16
Deposition Author(s): Boer, D.R., Uson, I., Coll, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.212
R-Value Work: 0.187
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Self-Assembly of Functionalizable Two-Component 3D DNA Arrays through the Induced Formation of DNA Three-Way-Junction Branch Points by Supramolecular Cylinders.

Boer, D.R., Kerckhoffs, J.M., Parajo, Y., Pascu, M., Uson, I., Lincoln, P., Hannon, M.J., Coll, M.

(2010) Angew Chem Int Ed Engl 49: 2336-2339

PubMed: 20191645 Search on PubMed
DOI: https://doi.org/10.1002/anie.200906742
Primary Citation of Related Structures:
3FX8, 3I1D

Organizational Affiliation

Institute for Research in Biomedicine and Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain.

Macromolecule Content

Total Structure Weight: 2.82 kDa
Atom Count: 182
Modelled Residue Count: 6
Deposited Residue Count: 6
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
(5'-D(CPGPTPAPCPG)-3'	A [auth C]	6	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5PM Query on 5PM Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain G [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C]	F [auth C], G [auth C]	4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline} C₂₄ H₁₈ N₄ S KHOHHSYBCGDFBZ-XUIWWLCJSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Interactions & Density Focus chain F [auth C] Focus chain G [auth C]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain B [auth C] SDF format, chain C SDF format, chain D [auth C] SDF format, chain E [auth C] MOL2 format, chain B [auth C] MOL2 format, chain C MOL2 format, chain D [auth C] MOL2 format, chain E [auth C]	B [auth C], C, D [auth C], E [auth C]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain B [auth C] Focus chain C Focus chain D [auth C] Focus chain E [auth C] Interactions & Density Focus chain B [auth C] Focus chain C Focus chain D [auth C] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.212
R-Value Work: 0.187
R-Value Observed: 0.187
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.249	α = 90
b = 49.249	β = 90
c = 49.249	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
SHELXDE	phasing
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Boer, D.R.

Uson, I.

Coll, M.

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources